Reactions Searchable

What is needed for progress in achieving a deeper insight into biochemical pathways is to allow all this information to be searchable by electronic means in other words, it has to be stored in a reaction database. 

All this information is now directly. searchable. All chemical species can be searched not only by name, but also by structure and substructure, and by their role in a reaction. Reactions can be searched by all the species involved but also by the types of atoms and bonds contained in the reaction center,... 

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. 

CAS REACT The Chemical Abstracts Research Service Information from 1985. Covers single and multistep reactions. Includes CAS Registry numbers of reactants, products, reagents, catalysts and solvents. It is structure searchable. 

Several databases of published biotransformations are commercially available, such as Molecular Design Ltd s Metabolite and the Accelerys Metabolism Database (formerly produced by Synopsis). The former is quite extensive, and contains in vivo and in vitro biotransformation summaries from the literature, while the latter has as its core information based on the U.K. Royal Society of Chemistry s Biotransformations series (Hawkins, 1988-1996) supplemented by additional data from the literature. Both systems are searchable by reaction type. The intelligent use of such databases provides much valuable information on likely metabolic profile. 

CASREACT is a structure and text-searchable organic chemical reaction database containing more than 17 million single- and multistep reactions with more than six hundred thousand records from journal articles and patents with reaction information. Coverage is from 1840 to the present. 

These two bulletins are issned monthly by the Royal Society of Chemistry, and each contain about 250 items per issue. Methods in Organic Synthesis (MOS) gives reaction schemes for new synthetic methods reported in the cnrrent literatnre, while Natnral Prodncts Update (NPU) covers papers dealing with the isolation, strnctnre determination, and synthesis of natnral prodncts. In each case, subscribers have access to the searchable web version. 

Each chemical reaction has a Reaxys Rx-ID, which is a unique registry number in this database, and is fully searchable. The table view of the records listed also presents possible synthesis route(s) of reactions with possible yield, conditions, and references. Results can be sorted, and redefined by filters. 

Science of Synthesis, multi-authored, Thieme Verlag. The subscription electronic version of Houben-Weyl, originally an exhaustive multivolume German language encyclopedia of synthetic methods. The printed version eventually contained 146,000 procedures, 580,000 structures, and 700,000 references. SoS retains the readable-text format of the original, with extensive HTML and structure markup for searchability. The current version (3.6) consists of 38 volumes and 215,000 reactions (www.science-of-synthesis.com). 

Synthesis library with about 70,000 searchable reactions from the literature. Macintosh, Silicon Graphics, and VAX. 

Products/technologies Index Chemicus database allows access to important reaction diagrams, full bibliographic information, full-length author abstracts, and a variety of searchable indices published in one substructure- and text-searchable database. 

Index Chemicus 1991-. Philadelphia, PA Institute for Scientific Information. Monthly. A text and substructure-searchable database with coverage of over one million structures published in the literature. Contains reaction diagrams... 

Synthetic Methodology Assessment for Reduction Techniques (SMART) A program adapted from the EPAs SMART review process and designed to quantify and categorize hazardous materials used in a manufacturing process. Green Synthetic Reactions Provides a searchable database of synthetic processes and identifies alternative processes published to replace more hazardous materials with less hazardous ones. 

Searchable data bases have for some time now simplified the search for the more routine methods of 7-membered ring synthesis. For this reason it seems reasonable to omit yet further examples of cyclisation by cyclocondensation or intramolecular Friedel-Crafts reaction, as well as new examples Schmidt and Beckmann ring expansion reactions, unless specific mechanistic or stereochemical features are of interest. 

Not only have the authors collected the data and put It in a searchable format, they have also classified all the reactions according to mechanism, t.e. the catalytic cycle, and this is easily accessible. This is of enormous value because it means the database can be searched from the point of view of the reagents, the reaction products, or the... 

One of the few examples of commercially available retrieval systems encompassing both compounds and reactions is Molecular Design s microcomputer-based ChemBase system. It saves molfiles (molecular structure files) separately from its reaction file without any elaborate linkages between the files. This makes it rather difficult to move information between the files and requires the conversion of a molfile to move it in or out of a reaction file. Additionally, searching a compound structure for where it appears in a reaction is not a simple operation. Lastly, reaction sites are neither identified nor searchable. These limitations could be overcome if the reaction site could be associated with the molfiles or reaction files stored for searching. 

Another microcomputer-based retrieval system, aimed at compounds as well as reactions is ChemSmart. This system saves a compound as a separate file associated with its own two-page notebook. Within the design mode there is a mechanism for labelling one or more atoms in the structure, but these are not searchable as of yet. ChemSmart uses compound files directly to define a reaction s reactants and products, and then associates the reaction with its own reaction notebook. The only way to label a reaction site presently in ChemSmart, is to label the reaction site fragments in the compounds used in the reaction. The labelled atom positions will show the label even in the reaction display. However, the reaction cannot be searched for the compounds present in it, or the presence of this labelled reaction site. The reaction site can be used as a query for substructural search on the compounds, if the compounds can be saved in the search file. The reaction display modide can take compounds from either the searchable or non-searchable files, so this is not a final solution. Even if the reaction site could be found quickly by using the reaction site as a substructure for compound... 

The optimal solution would be to have the reaction site saved in a searchable format. A reaction site is smaller than a molecule and, therefore, more space efficient. Also, smaller files will search faster and provide for greater data compression. One reaction site can be associated with a number of compounds and reactions. 

Reaction notes are input by the document analyst to report reaction conditions that are important and cannot be seen from the reaction participants safety information associated with the reaction or other reaction-related information. Reaction conditions are described by terms such as photochem or high pressure . The reaction note is searchable. 

Besides the data derived from the schemes, the metafiles (the pure graphic) and, of course, the data from the textual input (title, abstract, bibliographic data) will also be stored in the base file. This will be the source for indexes or subfiles, and for reaction databases for existing retrieval systems. As far as the used retrieval system will allow, all of these data except the display-only graphic metafile may be searchable. 

Crossfire is usually searched by drawing a chemical structure or reaction. It is also searchable by identifying elements, such as chemical name, name fragment, CAS RN, and molecular formula, as well as by numeric and keyword searches in various data fields. Crossfire, which will be fully replaced by a... 

A database is available with over 200 new entries and updates every year. It is fully searchable by structure, substructure and reaction type and allows sophisticated full text searches. http //www.mrw.interscience.wiley.com/eros/... 

Having these reactions collected in a single searchable tool is of immense value particularly to the synthetic chemist, but also to all academic institutions Involved in the Pharmaceutical and Chemical industry in general. 

Multi-step reactions as part of searchable databases can come in several forms. A reaction scheme recorded within one document (such as a total synthesis, or a multi-step procedure for performing a single transformation) is called an explicit scheme this type is the most common, and perhaps the most important. A scheme consisting of reactions assembled from different documents is called an implicit scheme, and can be located by a computer program, rather than being a record of experimental fact. Implicit schemes can be used to discover new routes to synthetic targets, and can in principle extend the utility of databases of reactions. 

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